Graphic Model-based Gene Regulatory Network Reconstruction using RNA Sequencing Count Data

Authors

  • Liliana Lopez-Kleine Universidad Nacional de Colombia - sede Bogotá
  • Cristian Andres Gonzalez-Prieto Universidad Nacional de Colombia

DOI:

https://doi.org/10.24297/jbt.v8i0.8298

Keywords:

Gene Regulatory Network, RNA-Seq, Graphical model, Negative Binomial Distribution, Overdispersion, Networks

Abstract

Interactions between genes, such as regulations are best represented by gene regulatory networks (GRN). These are often constructed based on gene expression data. Few methods for the construction of GRN exist for RNA sequencing count data. One of the most used methods for microarray data is based on graphical Gaussian networks. Considering that count data have different distributions, a method assuming RNA sequencing counts distribute Poisson has been proposed recently. Nevertheless, it has been argued that the most likely distribution of RNA sequencing counts is not Poisson due to overdispersion. Therefore, the negative binomial distribution is much more likely. For this distribution, no model-based method for the construction of GRN has been proposed until now. Here, we present a graphical, model-based method for the construction of GRN assuming a negative binomial distribution of the RNA sequencing count data. The R code is available under request. We used the method proposed both on simulated RNA sequencing count data and on real data. The graph is showed, and its descriptive measurements were assessed. They were found some interesting biological conclusions. We confirm that using negative binomial distribution for fitting the model is suitable because RNA sequencing data present overdispersion.

Downloads

Download data is not yet available.

Downloads

Additional Files

Published

2019-05-30

How to Cite

Lopez-Kleine, L., & Gonzalez-Prieto, C. A. (2019). Graphic Model-based Gene Regulatory Network Reconstruction using RNA Sequencing Count Data. JOURNAL OF ADVANCES IN BIOTECHNOLOGY, 8, 1078-1085. https://doi.org/10.24297/jbt.v8i0.8298

Issue

Section

Articles